As shown in his presentation, (at least this part is true), the autopilot is disconnected and any manoeuvers, (TCAS, GPWS, etc) are manually flown.
So you receive a TCAS RA
Absolutely it is you on the controls
You cannot see the other aircraft - you are trusting the software has not been hacked and the 'CLIMB CLIMB' has not been swapped with a 'DESCEND DESCEND'
Or perhaps the EGPWS alert is routed to the 'bit bucket' so you hear nothing despite the terrain that you are close to because the FMC has carried out a completely invalid QFF correction.
This exploit should not be underestimated.